Welcome to Autopia! I think you'll find that there is a wealth of knowledge here that will help you on your quest for the ideal finish on your Benz.
I'm assuming since you used the Meg's three-step system that you did it all by hand. If that's the case, then it's not too surprising that scratches still remain. To help reduce/eliminate the deeper defects you'll need a machine (like the Porter Cable 7424 or Ultimate Detailing Machine). MB clear tends to be pretty hard, so getting scratches and heavy swirls out can take some effort. The 2001 MB you have may be prior to the "cerami-clear" finish that MB currently uses, but even if it isn't you'll still need a reasonably strong combo to remove the heavier defects. Most folks will likely recommend the Menzerna line of polishes (Super Intensive Polish and Nano Polish).
Ultimately, the amount of effort you'll put in to remove defects is up to you. Does you car need to pass the 10 ft. rule? Five foot rule? Or do you want o be on top of it and see a flawless finish? Remember most people don't even notice swirls (except for us Autopians), so decide on a level that you're happy with and work towards it.
Good luck!